PacBio AD Pilot: Differential Isoform Expression with Kallisto Counts

Raw Counts

Filter Counts

Keep transcripts with at least 2 samples that have >= 10 counts

Covariate Data for DESeq2

Design Formula

~condition

Run DESeq2

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Add Gene Names to Differential Expression Results

Rows: 385669 Columns: 8
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (6): transcript_id, gene_id, gene_symbol, gene_version, chr, strand
dbl (2): start, end

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Volcano Plot of Differentially Expressed Isoforms [Labelled with Gene Name]

Padj threshold = 0.05

Log2FC threshold = +/- 1.5

Warning: Removed 220 rows containing missing values or values outside the scale range (`geom_point()`).

Error in filter(., !is.na(gene_label)) : 
  ensembldb::filter requires an 'EnsDb' object as input. To call the filter function from the stats or dplyr package use stats::filter and dplyr::filter instead.

Individual Isoform Count Plots by Condition and Sex

PCA on vst Normalized Counts

using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance